On 10/23/2017 09:47 AM, Martin Morgan wrote:
On 10/23/2017 09:26 AM, Elizabeth Purdom wrote:
Hello,
I am updating an existing package and I am getting an error in running
my vignette (and a similar error in an example in help pages) but ONLY
when I run R CMD BUILD. I can’t recreate the error in any session
where I can debug and figure out what is happening. So my question is
how can I recreate the exact environment of R CMD BUILD that runs the
vignette but in an interactive session so that I can figure out what
is going on?
I have tried reproducing the error in other environments:
* Running R —vanilla interactively and trying the code manually
* running purl on my vignette to get pure R code and running just the
R code with R CMD BATCH —vanilla
hint on the specific package and / or error message?
My approach would be to install the package, Stangle / purl the
vignette, and R -f vignette.R, then trim the vignette to a fast
reproducible case. But it sounds like you're doing that...
A little bit more helpfully, at least on Linux R CMD build evaluates the
script R_HOME/bin/build, which launches R as
echo 'tools:::.build_packages()' | R_DEFAULT_PACKAGES= LC_COLLATE=C
"${R_HOME}/bin/R" --no-restore --slave --args ${args}
It's actually very tedious to figure out how the R process that builds
the vignette is launched.
Martin
Martin
* Running R —vanilla interactively and compiling the vignette
But all of the above runs the code without any error.
Furthermore, for some reason TravisCI can build the package without
problem nor does it hit any error in R CMD CHECK with TravisCI so for
a long time I assumed it was some local file or environment on my
machine and forgot about it. But now that I have pushed the changes to
Bioconductor, they are getting the same error about the vignette not
building.
By the way, I can’t slowly take back my commands to see what broke it,
because the change was a dramatic one involving redefining my S4
class, so a large number of things had to be adapted before any code
would work and there’s no way to slowly roll that back.
Most of the posts I have seen about debugging discrepancies between R
CMD BUILD (or equivalently R CMD CHECK) seem to be about namespace
issues with other packages. Of course I can’t be sure since I have a
pretty terse error from R CMD BUILD, but the error that is given is my
own error (it’s a check I wrote as part of the validity check when I
updated the class) so it seems unclear how it would be a namespace error.
Thanks for any suggestions,
Elizabeth Purdom
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